5HT2 receptors have low affinity for serotonin (5-HT) and do not show receptor supersensitivity following lesion of nerve ending. We have proposed for the existence of an endogenous ligand (endocoid) for his receptor site. Our previous studies have demonstrated that some protein fractions derived from bovine and rat brains display activity of inhibiting 3H-Ketanserin binding but inhibiting only slightly 3H-mianserin binding to rat brain membrane. This protein (Mr=6000) has been partially purified by gel filtration and HPLC column chromatography. The present studies show the two 3H-ketanserin recognition sites are present in rat striatum as revealed by autoradiography and nonlinear, least square regression algorythm. The high affinity site (Kd 0.4 nM) is similar to the 5-HT2 site previously characterized by various investigators. The low affinity site (Kd 20 nM) has a unique pharmacological specificity and is preferentially localized to rat striatum and septum. A series of conventional 5-HT2 receptor antagonists, 5-HT and 5-HT uptake blockers are ineffective at inhibiting 3H-ketanserin binding to this low affinity site. Also, chronic treatment with p- chlorophenylalanine, which deplets brain 5-HT, up-regulates only the high affinity site. Moreover, selective lesion of 5-HT nerve ending with a neurotoxin failed to affect this low affinity binding sites. Thus, in the straitum and septum, 3H-ketanserin labels a unique recognition site. This site has recently been shown to be associated with dopaminergic nerve endings and may regulate biogenic amine release through recognition by some endogenous ligand. The present findings may shed light on the role of this peptide endocoid in the modulation of neurotransmission.